IMPORTANT NOTE: If the system is non-periodic (in a dimension), then +you should not make the lo/hi box dimensions (as defined in your +region command) radically smaller/larger than the extent +of the atoms you eventually plan to create, e.g. via the +create_atoms command. For example, if your atoms +extend from 0 to 50, you should not specify the box bounds as -10000 +and 10000. This is because LAMMPS uses the specified box size to +layout the 3d grid of processors. A huge (mostly empty) box will be +sub-optimal for performance when using "fixed" boundary conditions +(see the boundary command). When using "shrink-wrap" +boundary conditions (see the boundary command), a huge +(mostly empty) box may cause a parallel simulation to lose atoms the +first time that LAMMPS shrink-wraps the box around the atoms. +
Restrictions:
An atom_style and region must have diff --git a/doc/create_box.txt b/doc/create_box.txt index 9a249f1bf3..ccd9470d87 100644 --- a/doc/create_box.txt +++ b/doc/create_box.txt @@ -56,6 +56,20 @@ non-zero, then both the x and y dimensions must be periodic. Similarly, x and z must be periodic if xz is non-zero and y and z must be periodic if yz is non-zero. +IMPORTANT NOTE: If the system is non-periodic (in a dimension), then +you should not make the lo/hi box dimensions (as defined in your +"region"_region.html command) radically smaller/larger than the extent +of the atoms you eventually plan to create, e.g. via the +"create_atoms"_create_atoms.html command. For example, if your atoms +extend from 0 to 50, you should not specify the box bounds as -10000 +and 10000. This is because LAMMPS uses the specified box size to +layout the 3d grid of processors. A huge (mostly empty) box will be +sub-optimal for performance when using "fixed" boundary conditions +(see the "boundary"_boundary.html command). When using "shrink-wrap" +boundary conditions (see the "boundary"_boundary.html command), a huge +(mostly empty) box may cause a parallel simulation to lose atoms the +first time that LAMMPS shrink-wraps the box around the atoms. + [Restrictions:] An "atom_style"_atom_style.html and "region"_region.html must have diff --git a/doc/read_data.html b/doc/read_data.html index 6d2f9e2bb5..da6f19d0bb 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -144,8 +144,11 @@ lo/hi values radically smaller/larger than the extent of the atoms. For example, if your atoms extend from 0 to 50, you should not specify the box bounds as -10000 and 10000. This is because LAMMPS uses the specified box size to layout the 3d grid of processors. A huge -(mostly empty) box will be sub-optimal for performance and may cause a -parallel simulation to lose atoms the first time that LAMMPS +(mostly empty) box will be sub-optimal for performance when using +"fixed" boundary conditions (see the boundary +command). When using "shrink-wrap" boundary conditions (see the +boundary command), a huge (mostly empty) box may cause +a parallel simulation to lose atoms the first time that LAMMPS shrink-wraps the box around the atoms.
The "extra bond per atom" setting should be used if new bonds will be diff --git a/doc/read_data.txt b/doc/read_data.txt index 93bb0b9fc5..c964d6fa86 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -141,8 +141,11 @@ lo/hi values radically smaller/larger than the extent of the atoms. For example, if your atoms extend from 0 to 50, you should not specify the box bounds as -10000 and 10000. This is because LAMMPS uses the specified box size to layout the 3d grid of processors. A huge -(mostly empty) box will be sub-optimal for performance and may cause a -parallel simulation to lose atoms the first time that LAMMPS +(mostly empty) box will be sub-optimal for performance when using +"fixed" boundary conditions (see the "boundary"_boundary.html +command). When using "shrink-wrap" boundary conditions (see the +"boundary"_boundary.html command), a huge (mostly empty) box may cause +a parallel simulation to lose atoms the first time that LAMMPS shrink-wraps the box around the atoms. The "extra bond per atom" setting should be used if new bonds will be